JP2005-243476A discloses, as a conventional fuel cell system, a fuel cell system of an anode gas non-circulation type in which unused anode gas discharged to an anode gas discharge passage is not returned to an anode gas supply passage. This conventional fuel cell system suppresses a reduction in output performance of fuel cells by performing a pulsating operation of increasing and reducing a pressure of the anode gas and supplying the anode gas at a flow rate higher than a required flow rate to the fuel cells to discharge impurities retained in the fuel cells to the outside of the fuel cells at the time of increasing the pressure.